Early returns indicate Mr Aoun and his allies have won at least 15 of 35 seats being contested in the Christian heartland of the third of four stages in the poll.
Meanwhile in the eastern Bekaa Valley, the pro-Syrian militant group Hizbollah and its allies picked up at least 10 seats.
There are fears that Mr Aoun’s lead will return Lebanon to the destructive form of factionalism it suffered three decades ago.
“I concede that Michel Aoun won, but these results will take us back to 1976 and will allow the Syrians to enter Lebanon all over again,” said Druze leader Walid Jumblatt, during a live interview on Lebanese television.
Mr Jumblatt conceded defeat in all 16 Christian seats up for grabs.
Lebanon’s opposition alliance, which led the campaign to end nearly three decades of Syrian occupation suffered a major setback in the third and most important round of the parliamentary election.
Official results will be released on Tuesday.
Mr Aoun, a long-time critic of Damascus, has recently formed an unlikely alliance with longtime Syrian allies, including the family of Defence Minister Michel Murr.
But against expectations, it swept the board in constituencies reserved for Christians in both the central Mount Lebanon region and the eastern Bekaa Valley.
Sunday’s electoral setback for the opposition alliance was a far cry from the first round in the capital two weeks ago in which it swept every seat.
Analysts saod the defeat of several prominent anti-Syrian, Christian politicians will complicate the next parliament’s task of charting Lebanon’s political future.
“The Christian extremists have vanquished the moderates,” said Mr Jumblatt.
He accused Mr Aoun of serving Syrian interests, even though Damascus forced him to spend 15 years in exile and he only returned to Lebanon last month.
The fierce battle between Mr Aoun’s Free Patriotic Current and the main opposition alliance for the Christian vote has prompted record voter turnout.
The four-round elections are the first free of Syria’s 29-year-long military presence and follows February’s assassination of five-time prime minister Rafiq Hariri which plunged Lebanon into turmoil.
The third round came as a UN special envoy met Syrian President Bashar al-Assad amid US claims Syrian intelligence agents remained in Lebanon despite the troop pullout in April.
On Friday US President George W Bush warned Damascus it needed to “not only remove their military, but to remove intelligence officers as well.”
On the same day, UN Secretary General Kofi Annan ordered a UN verification mission back to Lebanon to check on the accusation.